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DOE OSTI2016

SU-F-T-620: Development of a Convolution/Superposition Dose Engine for CyberKnife System

Purpose: Current CyberKnife treatment planning system (TPS) provided two dose calculation algorithms: Ray-tracing and Monte Carlo. Ray-tracing algorithm is fast, but less accurate, and also can’t handle irregular fields since a multi-leaf collimator system was recently introduced to CyberKnife M6 system. Monte Carlo method has well-known accuracy, but the current version still takes a long time to finish dose calculations. The purpose of this paper is to develop a GPU-based fast C/S dose engine for CyberKnife system to achieve both accuracy and efficiency. Methods: The TERMA distribution from a poly-energetic source was calculated based on beam’s eye view coordinate system, which is GPU friendly and has linear complexity. The dose distribution was then computed by inversely collecting the energy depositions from all TERMA points along 192 collapsed-cone directions. EGSnrc user code was used to pre-calculate energy deposition kernels (EDKs) for a series of mono-energy photons The energy spectrum was reconstructed based on measured tissue maximum ratio (TMR) curve, the TERMA averaged cumulative kernels was then calculated. Beam hardening parameters and intensity profiles were optimized based on measurement data from CyberKnife system. Results: The difference between measured and calculated TMR are less than 1% for all collimators except in the build-up regions. The calculated profiles also showed good agreements with the measured doses within 1% except in the penumbra regions. The developed C/S dose engine was also used to evaluate four clinical CyberKnife treatment plans, the results showed a better dose calculation accuracy than Ray-tracing algorithm compared with Monte Carlo method for heterogeneous cases. For the dose calculation time, it takes about several seconds for one beam depends on collimator size and dose calculation grids. Conclusion: A GPU-based C/S dose engine has been developed for CyberKnife system, which was proven to be efficient and accurate for clinical purpose, and can be easily implemented in TPS.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Generalized and Mechanistic PV Module Performance Prediction From Computer Vision and Machine Learning on Electroluminescence Images

Electroluminescence (EL) imaging of photovoltiac (PV) modules offers high-speed, high-resolution information about device performance, affording opportunities for greater insight and efficiency in module characterization across manufacturing, research and development, and power plant operations and management. Predicting module electrical properties from EL image features is a critical step toward these applications. In this article, we demonstrate quantification of both generalized and performance mechanism-specific EL image features, using pixel intensity-based and machine learning classification algorithms. From EL image features, we build predictive models for PV module power and series resistance, using time-series current-voltage (I-V) and EL data obtained stepwise on five brands of modules spanning three Si cell types through two accelerated exposures: damp heat (DH) (85°C/85% RH) and thermal cycling (TC) (IEC 61215). Overall, 195 pairs of EL images and I-V characteristics were analyzed, yielding 11700 individual PV cell images. A convolutional neural network was built to classify cells by the severity of busbar corrosion with high accuracy (95%). Generalized power predictive models estimated the maximum power of PV modules from EL images with high confidence and an adjusted-R 2 of 0.88, across all module brands and cell types in extended DH and TC exposures. Mechanistic degradation prediction was demonstrated by quantification of busbar corrosion in EL images of three module brands in DH, and subsequent modeling of series resistance using these mechanism-specific EL image features. For modules exhibiting busbar corrosion, we demonstrated series resistance predictive models with adjusted-R 2 of up to 0.73.

14 SOLAR ENERGY↗

DOE OSTI2025

Real-Time Wave Energy Converter Control Using Instantaneous Frequency

Wave Energy Converters (WECs) rely on effective Power Take-Off (PTO) control strategies to maximize energy absorption under dynamic sea conditions. Traditional hydrodynamic modeling techniques may require computationally intensive convolution calculations, making real-time control implementation challenging. This paper presents an alternative approach by leveraging instantaneous frequency estimation to dynamically adjust PTO damping in response to varying wave frequencies. Two real-time frequency estimation methods are explored: the Hilbert Transform (HT) and Phase-Locked Loop (PLL). The Hilbert Transform method provides accurate frequency tracking but introduces a delayed response due to its dependence on causal data. Conversely, the PLL approach demonstrates strong potential in frequency tracking but requires careful gain tuning, particularly in complex sea states. Comparative evaluations across multiple test cases—including sinusoidal variations, amplitude steps, frequency step changes, and real-world JONSWAP spectrum waves—highlight the strengths and limitations of each method. The two different PTO control techniques across the various frequency estimation methods were tested under real-sea states using a state-space model of a point-absorbing Wave Energy Converter. The Capture Width Ratio (CWR) is used as a performance metric, with results showing that the HT achieves a 10.6% improvement, while the PLL estimation yields a 0.9% improvement relative to the fixed parameter control baseline. These results highlight the effectiveness of real-time frequency estimation in improving energy absorption compared to static control parameters.

WEC control↗

DOE OSTI2017

On the arithmetic intensity of high-order finite-volume discretizations for hyperbolic systems of conservation laws

It has been conjectured that higher-order discretizations for partial differential equations will have advantages over the lower-order counterparts commonly used today. The reasoning is that the increase in arithmetic operations will be more than offset by the reduction in data transfers and the increase in concurrent floating-point units. To evaluate this conjecture, the arithmetic intensity of a class of high-order finite-volume discretizations for hyperbolic systems of conservation laws is theoretically analyzed for spatial discretizations from orders three through eight in arbitrary dimensions. Additionally, three cache models are considered: the limiting cases of no cache and infinite cache as well as a finite-sized cache model. Models are validated experimentally by measuring floating-point operations and data transfers on an IBM Blue Gene/Q node. Theory and experiments demonstrate that high-order finite-volume methods will be able to provide increases in arithmetic intensity that will be necessary to make better utilization of on-node floating-point capability.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Investigating power capping toward energy-efficient scientific applications: Investigating Power Capping toward Energy-Efficient Scientific Applications

The emergence of power efficiency as a primary constraint in processor and system design poses new challenges concerning power and energy awareness for numerical libraries and scientific applications. Power consumption also plays a major role in the design of data centers, which may house petascale or exascale-level computing systems. At these extreme scales, understanding and improving the energy efficiency of numerical libraries and their related applications becomes a crucial part of the successful implementation and operation of the computing system. In this paper, we study and investigate the practice of controlling a compute system's power usage, and we explore how different power caps affect the performance of numerical algorithms with different computational intensities. Further, we determine the impact, in terms of performance and energy usage, that these caps have on a system running scientific applications. This analysis will enable us to characterize the types of algorithms that benefit most from these power management schemes. Our experiments are performed using a set of representative kernels and several popular scientific benchmarks. Lastly, we quantify a number of power and performance measurements and draw observations and conclusions that can be viewed as a roadmap to achieving energy efficiency in the design and execution of scientific algorithms.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2016

MultispeQ Beta: a tool for large-scale plant phenotyping connected to the open PhotosynQ network

Large-scale high-throughput plant phenotyping (sometimes called phenomics) is becoming increasingly important in plant biology and agriculture and is essential to cutting-edge plant breeding and management approaches needed to meet the food and fuel needs for the next century. Currently, the application of these approaches is severely limited by the availability of appropriate instrumentation and by the ability to communicate experimental protocols, results and analyses. To address these issues, we have developed a low-cost, yet sophisticated open-source scientific instrument designed to enable communities of researchers, plant breeders, educators, farmers and citizen scientists to collect high-quality field data on a large scale. The MultispeQ provides measurements in the field or laboratory of both, environmental conditions (light intensity and quality, temperature, humidity, CO 2 levels, time and location) and useful plant phenotypes, including photosynthetic parameters—photosystem II quantum yield (Φ II ), non-photochemical exciton quenching (NPQ), photosystem II photoinhibition, light-driven proton translocation and thylakoid proton motive force, regulation of the chloroplast ATP synthase and potentially many others—and leaf chlorophyll and other pigments. Plant phenotype data are transmitted from the MultispeQ to mobile devices, laptops or desktop computers together with key metadata that gets saved to the PhotosynQ platform (https://photosynq.org) and provides a suite of web-based tools for sharing, visualization, filtering, dissemination and analyses. We present validation experiments, comparing MultispeQ results with established platforms, and show that it can be usefully deployed in both laboratory and field settings. We present evidence that MultispeQ can be used by communities of researchers to rapidly measure, store and analyse multiple environmental and plant properties, allowing for deeper understanding of the complex interactions between plants and their environment.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Strangers in a foreign land: ‘Yeastizing’ plant enzymes

Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

MaDaTS: Managing Data on Tiered Storage for Scientific Workflows

Scientific workflows are increasingly used in High Performance Computing (HPC) environments to manage complex simulation and analyses, often consuming and generating large amounts of data. However, workflow tools have limited support for managing the input, output and intermediate data. The data elements of a workflow are often managed by the user through scripts or other ad-hoc mechanisms. Technology advances for future HPC systems is redefining the memory and storage subsystem by introducing additional tiers to improve the I/O performance of data-intensive applications. These architectural changes introduce additional complexities to managing data for scientific workflows. Thus, we need to manage the scientific workflow data across the tiered storage system on HPC machines. In this paper, we present the design and implementation of MaDaTS (Managing Data on Tiered Storage for Scientific Workflows), a software architecture that manages data for scientific workflows. We introduce Virtual Data Space (VDS), an abstraction of the data in a workflow that hides the complexities of the underlying storage system while allowing users to control data management strategies. We evaluate the data management strategies with real scientific and synthetic workflows, and demonstrate the capabilities of MaDaTS. Our experiments demonstrate the flexibility, performance and scalability gains of MaDaTS as compared to the traditional approach of managing data in scientific workflows.

Ghoshal, Devarshi↗

DOE OSTI2016

Draco,Version 6.x.x

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

Thompson, Kelly↗

DOE OSTI2023

FrESCO

The National Cancer Institute (NCI) monitors population level cancer trends as part of its Surveillance, Epidemiology, and End Results (SEER) program. This program consists of state or regional level cancer registries which collect, analyze, and annotate cancer pathology reports. From these annotated pathology reports, each individual registry aggregates cancer phenotype information and summary statistics about cancer prevalence to facilitate population level monitoring of cancer incidence. Extracting cancer phenotype from these reports is a labor intensive task, requiring specialized knowledge about the reports and cancer. Automating this information extraction process from cancer pathology reports has the potential to improve not only the quality of the data by extracting information in a consistent manner across registries, but to improve the quality of patient outcomes by reducing the time to assimilate new data and enabling time-sensitive applications such as precision medicine. Here we present FrESCO: Framework for Exploring Scalable Computational Oncology, a modular deep-learning natural language processing (NLP) library for extracting pathology information from clinical text documents.

Spannaus, Adam [Oak Ridge National Lab. (ORNL), Oa↗

DOE OSTI2016

PHYSICS OF ECLIPSING BINARIES. II. TOWARD THE INCREASED MODEL FIDELITY

The precision of photometric and spectroscopic observations has been systematically improved in the last decade, mostly thanks to space-borne photometric missions and ground-based spectrographs dedicated to finding exoplanets. The field of eclipsing binary stars strongly benefited from this development. Eclipsing binaries serve as critical tools for determining fundamental stellar properties (masses, radii, temperatures, and luminosities), yet the models are not capable of reproducing observed data well, either because of the missing physics or because of insufficient precision. This led to a predicament where radiative and dynamical effects, insofar buried in noise, started showing up routinely in the data, but were not accounted for in the models. PHOEBE (PHysics Of Eclipsing BinariEs; http://phoebe-project.org) is an open source modeling code for computing theoretical light and radial velocity curves that addresses both problems by incorporating missing physics and by increasing the computational fidelity. In particular, we discuss triangulation as a superior surface discretization algorithm, meshing of rotating single stars, light travel time effects, advanced phase computation, volume conservation in eccentric orbits, and improved computation of local intensity across the stellar surfaces that includes the photon-weighted mode, the enhanced limb darkening treatment, the better reflection treatment, and Doppler boosting. Here we present the concepts on which PHOEBE is built and proofs of concept that demonstrate the increased model fidelity.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Draco,Version 6.x.x

Thompson, Kelly↗

DOE OSTI2025

Flexible and Effective Object Tiering for Heterogeneous Memory Systems

Computing platforms that package multiple types of memory, each with their own performance characteristics, are quickly becoming mainstream. To operate efficiently, heterogeneous memory architectures require new data management solutions that are able to match the needs of each application with an appropriate type of memory. As the primary generators of memory usage, applications create a great deal of information that can be useful for guiding memory management, but the community still lacks tools to collect, organize, and leverage this information effectively. To address this gap, this work introduces a novel software framework that collects and analyzes object-level information to guide memory tiering. The framework includes tools to monitor the capacity and usage of individual data objects, routines that aggregate and convert this information into tier recommendations for the host platform, and mechanisms to enforce these recommendations according to user-selected policies. Moreover, the developed tools and techniques are fully automatic, work on standard Linux systems, and do not require modification or recompilation of existing software. Using this framework, this study evaluates and compares the impact of a variety of design choices for memory tiering, including different policies for prioritizing objects for the fast memory tier as well as the frequency and timing of migration events. In conclusion, the results, collected on a modern Intel platform with conventional DDR4 SDRAM as well as Intel Optane NVRAM, show that guiding data tiering with object-level information can enable significant performance and efficiency benefits compared with standard hardware- and software-directed data-tiering strategies for a diverse set of memory-intensive workloads.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

A new development on measurement and control software of SANS BATAN spectrometer (SMARTer) in Serpong, Indonesia

In 2005, the main computer for data acquisition and control system of Small-angle Neutron Scattering (SANS) BATAN Spectrometer (SMARTer) was replaced since it halted to operate the spectrometer. According to this replacement, the new software for data acquisition and control system has been developed in-house. Visual Basic programming language is used in developing the software. In the last two years, many developments have been made both in the hardware and also the software to conduct the experiment is more effective and efficient. Lately, the previous motor controller card (ISA Card) was replaced with the programmable motor controller card (PCI Card) for driving one motor of position sensitive detector (PSD), eight motors of four collimators, and six motors of six pinhole discs. This new control system software makes all motors can be moved simultaneously, then it reduces significantly the consuming time of setting up the instrument before running the experiment. Along with that development, the new data acquisition software under MS Windows operating system is also developed to drive a beam stopper in X-Y directions as well as to read the equipment status such as position of the collimators and PSD, to acquire neutron counts on monitor and PSD detectors, and also to manage 12 samples position automatically. A timer object which is set in one second to read the equipment status via serial port of the computer (RS232C), and general purpose interface board (GPIB) for reading the total counts of each pixel of the PSD from histogram memory was used in this new software. The experiment result displayed in real time on the main window, and the data is saved in the special format for further data reduction and analysis. The new software has been implemented and performed for experiment using a preset count or preset time mode for absolute scattering intensity method.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2017

Final Report: Quantification of Uncertainty in Extreme Scale Computations (QUEST)

QUEST (\url{www.quest-scidac.org}) is a SciDAC Institute that is focused on uncertainty quantification (UQ) in large-scale scientific computations. Our goals are to (1) advance the state of the art in UQ mathematics, algorithms, and software; and (2) provide modeling, algorithmic, and general UQ expertise, together with software tools, to other SciDAC projects, thereby enabling and guiding a broad range of UQ activities in their respective contexts. QUEST is a collaboration among six institutions (Sandia National Laboratories, Los Alamos National Laboratory, the University of Southern California, Massachusetts Institute of Technology, the University of Texas at Austin, and Duke University) with a history of joint UQ research. Our vision encompasses all aspects of UQ in leadership-class computing. This includes the well-founded setup of UQ problems; characterization of the input space given available data/information; local and global sensitivity analysis; adaptive dimensionality and order reduction; forward and inverse propagation of uncertainty; handling of application code failures, missing data, and hardware/software fault tolerance; and model inadequacy, comparison, validation, selection, and averaging. The nature of the UQ problem requires the seamless combination of data, models, and information across this landscape in a manner that provides a self-consistent quantification of requisite uncertainties in predictions from computational models. Accordingly, our UQ methods and tools span an interdisciplinary space across applied math, information theory, and statistics. The MIT QUEST effort centers on statistical inference and methods for surrogate or reduced-order modeling. MIT personnel have been responsible for the development of adaptive sampling methods, methods for approximating computationally intensive models, and software for both forward uncertainty propagation and statistical inverse problems. A key software product of the MIT QUEST effort is the MIT Uncertainty Quantification library, called MUQ (\url{muq.mit.edu}).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

JSPEC – An Open Source Program for IBS and Electron Cooling Simulation

The intrabeam scattering can affect the accumulation, the lifetime, and the property of a high-intensity beam. Electron cooling is a method to mitigate the intrabeam scattering effect. JSPEC (JLab Simulation Package on Electron Cooling) is an open-source program developed at Jefferson Lab, which includes various numerical models and friction force formulas for intrabeam scattering and electron cooling simulations. JSPEC has been benchmarked with BETACOOL and experimental data. In this report, we will introduce what features JSPEC provides to the users and how it carries out the computations. Numerical examples are presented to demonstrate the performance and the validity of JSPEC.

Zhang, He↗

DOE OSTI2024

Real World Use Case Evaluation of Radar Retro-reflectors for Autonomous Vehicle Lane Detection Applications

Lane detection plays a critical role in autonomous vehicles for safe and reliable navigation. Lane detection is traditionally accomplished using a camera sensor and computer vision processing. The downside of this traditional technique is that it can be computationally intensive when high quality images at a fast frame rate are used and has reliability issues from occlusion such as, glare, shadows, active road construction, and more. This study addresses these issues by exploring alternative methods for lane detection in specific scenarios caused from road construction-induced lane shift and sun glare. Specifically, a U-Net, a convolutional network used for image segmentation, camera-based lane detection method is compared with a radar-based approach using a new type of sensor previously unused in the autonomous vehicle space: radar retro-reflectors. This evaluation is performed using ground truth data, obtained by measuring the lane positions and transforming them into pixel coordinates. The performance of each method is assessed using the statistical R2 score, indicating the correlation between the detected lane lines and the ground truth. The results show that the U-Net camera-based method exhibits limitations in accurately detecting and aligning the lane lines, particularly in challenging scenarios. However, the radar-based lane detection method demonstrates a strong correlation with the ground truth which implies that the use of this sensor may improve current reliability issues from conventional camera lane detection approach. Furthermore, the study highlights the limitations of the U-Net model for camera lane detection, especially in scenarios with sun glare. This study shows that infrastructure-based radar retro-reflectors can improve autonomous vehicle lane detection reliability. The integration of different sensor modalities and the development of advanced computer vision algorithms are crucial for improving the accuracy, reliability, and energy efficiency of lane detection systems. Addressing these challenges contributes to the advancement of autonomous vehicles and the realization of safer and more efficient transportation systems.

Brown, Nicolas E.↗

DOE OSTI2013

On Eliminating Synchronous Communication in Molecular Simulations to Improve Scalability

Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

Straatsma, TP↗